As climate change intensifies environmental stresses on crops, threatening global food security, exploring internal biological mechanisms that enhance plant resilience becomes increasingly critical. In this thesis, we investigated the role of seed-transmitted endophytic bacteria in increasing the resilience and health of Solanum lycopersicum, using a sterile hydroponic system. We designed a novel peptide nucleic acid clamp, specific to S. lycopersicum var. Moneymaker, to reduce co-amplification of plant DNA during PCR amplification of the 16S-ITS-23S rrn operon of endophytic bacteria and established a new bioinformatic pipeline for species-level metagenomic analysis, PRONAME. This approach allowed us to identify core microbiota transmitted through seeds in three organs of plants: seed, roots, and shoots. This core microbiota includes Ralstonia, Sphingomonas, Bradyrhizobium, Roseateles, Microbacterium, and Stenotrophomonas. Our study further examined how these endophytes could enhance osmotic stress tolerance in tomatoes by characterizing the ecological properties of cultural endophytic bacteria, using culture-dependent methods for both in vitro and in planta assays. The creation of mCherry-tagged strains of previously isolated Pseudomonas enabled precise tracking of these bacteria, verifying their capacity for endophytic colonization within both shoots and roots. Additionally, we observed the impact of osmotic stress and humic substances (HS) treatment on the root endophytic community's composition. Our findings highlight the dynamic interactions between HS and endophytic bacteria under osmotic stress, demonstrating that HS not only directly improves tomato resilience to stress but also modulates root-associated microbial communities. This synergistic effect emphasizes the potential of integrating the microbial dimension into biostimulant research, advocating for a holistic approach that views the plant as a holobiont.